The wantaway striker had flown out to Thailand with the rest of the squad and was expected to feature in David Moyes' first game in charge against Singha All-Star XI on Saturday.
However, the 27-year-old suffered an injury during the first day of training and will fly home immediately from the three-week trip, with the club confirming he will need "further assessment and rehabilitation".
"Gutted to have picked up a niggling injury especially as training was going so well," Rooney wrote on his Facebook page.
"Heading back to Manchester to have it assessed fully but early indications are nothing to worry about."
United's medical team expect Rooney to be unavailable for four weeks, which has cast doubts over his participation in the club's Community Shield clash with Wigan and their opening Premier League game of the season against Swansea City.
Rooney's future at Old Trafford is still uncertain after handing in a second transfer request in three years at the end of last season.
However, new manager David Moyes used his first press conference as United boss to insist the striker would be staying at the club.